I have a site with about 1600 pages indexed by Google and only 200 are not included in the Supplementals. If someone experienced in this field could offer their advice, please shoot me a PM as I don't want to disclose my URL here. Cheers.
If the pages are not original content, but duplicate content, supplemental results is normal. If your pages are original content, try unique titles and (meta descriptions of at least 70 characters).
Also, depending on the content 200/1600 isn't really that bad. That's 12.5%, I've got sites hovering around 5% that I'm pretty happy to have gotten there (over 30,000 pages). But yes, unique content. Try to differentiate titles, h1 (maybe?), meta desc/keyword, and on page content.
My advise is try look at this site http://www.seo4fun.com/notes/supplementals.html. I hope it will help you.